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MEDME specifications

Information


Unique identifier OMICS_00614
Name MEDME
Alternative name Modeling Experimental Data with MeDIP Enrichment
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.40.0
Stability Stable
Requirements
methods, stats, graphics, utils, Biostrings, grDevices, R(>=2.15), BSgenome.Hsapiens.UCSC.hg18, MASS, drc, BSgenome.Mmusculus.UCSC.mm9
Maintained Yes

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Documentation


Maintainer


  • person_outline Mattia Pelizzola <>

Publication for Modeling Experimental Data with MeDIP Enrichment

MEDME in publications

 (12)
PMCID: 4944166
PMID: 27411928
DOI: 10.1038/srep29390

[…] samples, the log2 ratio obtained from raw data values should be normalised. we performed median centering, quantile normalisation and linear smoothing using bioconductor packages ringo, limma and medme., from the normalised log2 ratio data, a sliding-window (750 bp) peak-finding algorithm provided by nimblescan v2.5 (roche-nimblegen) was applied to analyse the medip-chip data. a one-sided […]

PMCID: 4852908
PMID: 27136348
DOI: 10.1371/journal.pone.0154836

[…] various metabolite and protein binding domains, as well as membrane channels ()., affected pathways and genes identified using both partek and ipa network analysis software., medip-chip and medme analysis identified a total of 4640 dmrs in gene promoters (defined as -5000 to 0 bp relative to the transcriptional start site) or gene bodies at ams p-value<0.01. of these dmrs, 82% […]

PMCID: 4692407
PMID: 26709917
DOI: 10.1371/journal.pone.0145585

[…] wi, usa). raw data was extracted as pair files by nimblescan software. median centering, quartile normalization, and linear smoothing were conducted using the bioconductor packages ringo, limma, and medme, respectively. peak-finding algorithm is provided by nimblescan v2.5 (roche-nimblegen). a one-sided kolmogorov-smirnov (ks) test is applied for peak finding following manufacture’s guide. peaks […]

PMCID: 4487197
PMID: 26137221
DOI: 10.1186/s40303-015-0013-5

[…] for 19 days., raw data generated from scans were normalized (log2-ratio). it followed median centering, quantile normalization and linear smoothing using bioconductor packages ringo, limma, and medme. the results were used in a sliding-window (750 bp) peak-finding algorithm provided by nimblescan v2.5 (roche-nimblegen). a one-sided kolmogorov-smirnov (ks) test is applied to determine […]

PMCID: 4494167
PMID: 25943100
DOI: 10.1186/s12920-015-0093-1

[…] as 22,532 promoters of the refseq genes derived from the ucsc refflat files. median-centering, quantile normalization, and linear smoothing was performed by bioconductor packages ringo, limma, and medme at arraystar. lastly, in order to compare the two groups’ differentially enriched regions the average of the log2-ratio values for each group (i.e. experimental patient [e] and healthy control […]


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MEDME institution(s)
Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA; Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
MEDME funding source(s)
The Yale Spore in Skin Cancer funded by the National Cancer Institute grant number 1 P50 CA121974; the National Library of Medicine grant K22LM009255; the National Cancer Institute grant K22CA123146-2

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